PhysioDesigner
A modeling tool for multilevel physiological systems

Oct 2013

Version 1.0 beta6

PhysioDesigner 1.0 beta6


20th Octorber, 2013

Install Note

Mac: Once you mount the disk image file you download, you will find a directory named "PhysioDesigner1.0b6". Please move the directory anyplace you want to put. That's all for installation.

Note 1) PhysioDesigner cannot be launched from the dmg mounted volume because of the lack of write permission of the volume. It is necessary to copy PhysioDesigner1.0b6 directory (which include PhysioDesigner.app, Morphology.app etc) somewhere on your local file system such as /Applications.

Note 2) If launch process fails, please try to remove $Users/.physiodesigner directory where some configuration related to PhysioDesigner are stored. By removing this file, configurations are reset to the default.

Note 3) Directory structure in PhysioDesigner1.0b6 is crucial for execution of PhysioDesigner.app and other apps. For example, all apps and server directly must be in the same directly.

Note 4) To install PhysioDesigner into Mountain Lion (OSX 10.8), users need to change the system preferences so that any applications (from other than Mac App Store) can be installed. Check System Preferences > Security & Privacy > General. "Allow applications downloaded from Anywhere".

Win: Please execute the installer by double clicking it. It installs a couple of necessary libraries such as Python, etc.

Note 1) On Windows XP with full windows update, Python 2.7 can cause problem, consequently PhysioDesigner cannot work, because PhysioDesigner depends on Python. So far we could not solve this issue. But if Python can work properly, PhysioDesigner itself should run OK.

Release Notes

On PhysioDesigner
Morphospace is implemented for interactive modelling in 3D space with morphological data, which can be called from Window in the menu bar.
Objects can be created, modified and deleted in Morphospace. Of course those objects can move and rotate.
Corresponding module can be found in logical canvas and vice versa.
Find module / physical quantity function was enhanced.
Zoom in/out of the logical canvas was improved.
The order of ports on a module can be swapped by long-click on the port.
Several bugs were fixed.

On ImageViewer
Now it is possible to select voxels interactively in ImageViewer. 
Selected voxels are stored in xml file for further utilization.
Brain dipole and arbitrary markers can be set color with a color dialog.
The way to visualize raw, mhd and vol format files were changed. Now each voxel is visualized as a cuboid.
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Linux el5.x86_64
Linux el6.x86_64
PhysioDesigner1.0b5_el5.x86_64.rpm
Note: These installers for linux are still experimental. If you noticed any problem on the installers, please contact us.


Flint 1.0 beta6


Flint can perform simulations of models created on PhysioDesigner.
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Linux el5.x86_64
Linux el6.x86_64
Note: These installers for linux are still experimental. If you noticed any problem on the installers, please contact us.

Install Note

Mac:
Note 1) To install PhysioDesigner into Mountain Lion (OSX 10.8), users need to change the system preferences so that any applications (from other than Mac App Store) can be installed. Check System Preferences > Security & Privacy > General. "Allow applications downloaded from Anywhere".

Release Notes

Added "Parameter" tab to view and modify parameters like initial values of ODE for next run of simulation
Support for PHML's DeltaTime function
Support for MathML elements <not> and <neq> in <piece>
Fix for importing external SBML model in PHML
Fix for submitting a simulation job to Flint K3